Homologous recombination impacts profoundly on the biology of Neisseria gonorrhoeae either through the rearrangement of specific gene sequences that encode surface antigens, or, by allowing unfettered exchange of chromosomal DNAs via horizontal transmission in vivo. Thus, recombination not only shuffles specific gene sequences, but also provides a means to disseminate the variant genetic information throughout a population. Consequently, large variant populations exist, that make therapeutic intervention difficult and impair the efficacy of many vaccine candidates. Therefore, it is the goal of this work to define more precisely, 1) the molecular mechanisms involved in the rearrangement of specific chromosomal loci (e.g. pilE the gene encoding the surface-exposed pilin polypeptide); and 2) examine the genetic limitations that may exist in the exchange of chromosomal DNAs between cells. It is hoped that these investigations may allow for novel therapeutic interventions.